Digital Commons Network^™

Pet191 Is A Cytochrome C Oxidase Assembly Factor In Saccharomyces Cerevisiae, Oleh Khalimonchuk, Kevin Rigby, Megan Bestwick, Fabien Pierrel, Paul A. Cobine, Dennis R. Winge

Department of Biochemistry: Faculty Publications

The twin-Cx₉C motif protein Pet191 is essential for cytochrome c oxidase maturation. The motif Cys residues are functionally important and appear to be present in disulfide linkages within a large oligomeric complex associated with the mitochondrial inner membrane. The import of Pet191 differs from that of other twin-Cx₉C motif class of proteins in being independent of the Mia40 pathway.

Coa2 Is An Assembly Factor For Yeast Cytochrome C Oxidase Biogenesis That Facilitates The Maturation Of Cox1, Fabien Pierrel, Oleh Khalimonchuk, Paul A. Cobine, Megan Bestwick, Dennis R. Winge

Department of Biochemistry: Faculty Publications

The assembly of cytochrome c oxidase (CcO) in yeast mitochondria is dependent on a new assembly factor designated Coa2. Coa2 was identified from its ability to suppress the respiratory deficiency of coa1 Δ and shy1 Δ cells. Coa1 and Shy1 function at an early step in maturation of the Cox1 subunit of CcO. Coa2 functions downstream of the Mss51-Coa1 step in Cox1 maturation and likely concurrent with the Shy1-related heme a₃ insertion into Cox1. Coa2 interacts with Shy1. Cells lacking Coa2 show a rapid degradation of newly synthesized Cox1. Rapid Cox1 proteolysis also occurs in shy1 Δ cells, suggesting …

Purification From Human Milk Of Matriptase Complexes With Secreted Serpins: Mechanism For Inhibition Of Matriptase Other Than Hai-1, I-Chu Tseng, Feng-Pai Chou, Sheng-Feng Su, Michael Oberst, Nandakumar Madayiputhiya, Ming-Shyue Lee, Jehng-Kang Wang, David E. Sloane, Michael Johnson, Chen-Yong Lin

Department of Biochemistry: Faculty Publications

Matriptase, a type 2 transmembrane serine protease, is predominately expressed by epithelial and carcinoma cells in which hepatocyte growth factor activator inhibitor 1 (HAI-1), a membrane-bound, Kunitz-type serine protease inhibitor, is also expressed. HAI-1 plays dual roles in the regulation of matriptase, as a conventional protease inhibitor and as a factor required for zymogen activation of matriptase. As a consequence, activation of matriptase is immediately followed by HAI-1-mediated inhibition, with the activated matriptase being sequestered into HAI-1 complexes. Matriptase is also expressed by peripheral blood leukocytes, such as monocytes and macrophages; however, in contrast to epithelial cells, monocytes and macrophages …

A Highly Conserved Family Of Inactivated Archaeal B Family Dna Polymerases, Igor Rogozin, Kira Makarova, Youri Pavlov, Eugene Koonin

Papers in Evolution

A widespread and highly conserved family of apparently inactivated derivatives of archaeal B-family DNA polymerases is described. Phylogenetic analysis shows that the inactivated forms comprise a distinct clade among archaeal B-family polymerases and that, within this clade, Euryarchaea and Crenarchaea are clearly separated from each other and from a small group of bacterial homologs. These findings are compatible with an ancient duplication of the DNA polymerase gene followed by inactivation and parallel loss in some of the lineages although contribution of horizontal gene transfer cannot be ruled out. The inactivated derivative of the archaeal DNA polymerase could form a complex …

Superfeminization As An Effect Of Bisphenol A In Marisa Cornuarietis & Response From Forbes Et Al. To Oehlmann Et Al., Jörg Oehlmann, Ulrike Schulte-Oehlmann, Jean Bachmann, Matthias Oetken, Ilka Lutz, Werner Kloas, Valery E. Forbes, John Aufderheide, Ryan Warbritton, Nelly Van Der Hoeven, Norbert Caspers

Valery Forbes Publications

[Oehlmann et al.]: Recently, we had the opportunity to read two articles in volume 66 of Ecotoxicology and Environmental Safety. Forbes et al. (2007a, , 2007b) declare “to explore the reproducibility of prior work” showing that bisphenol A (BPA) induces superfeminization in the freshwater snail Marisa cornuarietis (Oehlmann et al., 2000, 2006; Schulte- Oehlmann et al., 2001). Based on the outcome of a toxicity test with the same species, the authors conclude that their results “do not support previous claims of enhanced reproduction in M. cornuarietis in response to exposure to BPA.” We take issue with the declaration of …

Life History And Population Dynamics Of The Opportunistic Polychaete Capitella Sp. I In Relation To Sediment Organic Matter, Tina Ramskov, Valery E. Forbes

Valery Forbes Publications

Capitella sp. I is a deposit-feeding polychaete that occurs in estuarine and marine environments and that shows boom-bust population dynamics in response to organic pollution. A lifecycle experiment was carried out to quantify the relative importance of individual life-history traits for driving the dynamics of Capitella sp. I populations in response to changes in sediment organic matter concentrations. Individual-level effects were estimated as changes in survival, reproductive characteristics, and growth. Effects at the population-level were assessed by integrating the measured life-history traits in a simple 2-stage demographic model that was used to estimate the population growth rate (λ). Low organic …

Plankton Stress Responses From Pah Exposure And Nutrient Enrichment, Morten Hjorth, Valery E. Forbes, Ingela Dahllöf

Valery Forbes Publications

The hypothesis that the nature and force of PAH stress responses from plankton systems are coupled to the nutrient status of that system was tested in a mesocosm experiment. Four treatments were applied consisting of control (Cn), pyrene exposed (Py). nutrient spiked (Nu), and nutrient spiked and pyrene exposed (NuPy) groups in replicate bags (n = 3) representing plankton communities including bacteria, phytoplankton and zooplankton. Regardless of nutrient status, all the Py mesocosms were affected directly with decreases in chlorophyll α concentrations to 20 % of control values on Day 1. Primary production was also significantly lower (< 50 %) than Cn communities in both Py and NuPy communities after the first pyrene exposure. Indirect effects were observed as increased bacterial activity due to nutrient release from algal death, thereby channelling growth to another trophic level. With time the plankton system became top-down controlled, dominated by zooplankton, which was also the trophic group experiencing the longest lasting effect on structure. The occurrence of late effects in the zooplankton communities were seen in all treatments, but the magnitude of the effects was dependent on the nutrient status, most probably because of a larger trophic transfer of the contaminant. To improve our understanding of contaminant effects on food webs in natural communities, it is imperative that interactions between trophic levels in relation to abiotic factors are investigated.

Evolution Of Set-Domain Protein Families In The Unicellular And Multicellular Ascomycota Fungi, Chendhore Veerappan, Zoya Avramova, Etsuko N. Moriyama

School of Biological Sciences: Faculty Publications

Background: The evolution of multicellularity is accompanied by the occurrence of differentiated tissues, of organismal developmental programs, and of mechanisms keeping the balance between proliferation and differentiation. Initially, the SET-domain proteins were associated exclusively with regulation of developmental genes in metazoa. However, finding of SET-domain genes in the unicellular yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe suggested that SET-domain proteins regulate a much broader variety of biological programs. Intuitively, it is expected that the numbers, types, and biochemical specificity of SET-domain proteins of multicellular versus unicellular forms would reflect the differences in their biology. However, comparisons across the unicellular and multicellular …

Parasite-Mediated Disruptive Selection In A Natural Daphnia Population, Meghan Duffey, Chad Brassil, Spencer Hall, Alan Tessier, Carla Cáceres, Jeffrey Conner

School of Biological Sciences: Faculty Publications

Background: A mismatch has emerged between models and data of host-parasite evolution. Theory readily predicts that parasites can promote host diversity through mechanisms such as disruptive selection. Yet, despite these predictions, empirical evidence for parasite-mediated increases in host diversity remains surprisingly scant.
Results: Here, we document parasite-mediated disruptive selection on a natural Daphnia population during a parasite epidemic. The mean susceptibility of clones collected from the population before and after the epidemic did not differ, but clonal variance and broad-sense heritability of post-epidemic clones were significantly greater, indicating disruptive selection and rapid evolution. A maximum likelihood method that we developed …

Regulation Of Aromatic Alcohol Production In Candida Albicans, Suman Ghosh, Bessie W. Kebaara, Audrey L. Atkin, Kenneth W. Nickerson

School of Biological Sciences: Faculty Publications

Colonization by the fungal pathogen Candida albicans varies significantly, depending upon the pH and availability of oxygen. Because of our interest in extracellular molecules as potential quorum-sensing molecules, we examined the physiological conditions which regulate the production of the aromatic alcohols, i.e., phenethyl alcohol, tyrosol, and tryptophol. The production of these fusel oils has been well studied for Saccharomyces cerevisiae. Our data show that aromatic alcohol yields for C. albicans are determined by growth conditions. These conditions include the availability of aromatic amino acids, the pH, oxygen levels, and the presence of ammonium salts. For example, for wild-type C. …

Optimal Data Partitioning And A Test Case For Ray-Finned Fishes (Actinopterygii) Based On Ten Nuclear Loci, Chenhong Li, Guoqing Lu, Guillermo Ortí

School of Biological Sciences: Faculty Publications

Data partitioning, the combined phylogenetic analysis of homogeneous blocks of data, is a common strategy used to accommodate heterogeneities in complex multilocus data sets. Variation in evolutionary rates and substitution patterns among sites are typically addressed by partitioning data by gene, codon position, or both. Excessive partitioning of the data, however, could lead to overparameterization; therefore, it seems critical to define the minimum numbers of partitions necessary to improve the overall fit of the model. We propose a new method, based on cluster analysis, to find an optimal partitioning strategy for multilocus protein-coding data sets. A heuristic exploration of alternative …

Pea Aphid, Jennifer A. Brisson, Gregory K. Davis

School of Biological Sciences: Faculty Publications

Aphids have long been of interest because of their complex life cycles, environmentally induced morphologies, and importance to agriculture. However, only recently has the resulting wealth of ecological and population genetic data begun to be supplemented by genomic and genetic mapping approaches. In 2004, the International Aphid Genomics Consortium, a collaboration of aphid researchers, chose to establish the pea aphid, Acyrthosiphon pisum, as the aphid of choice for the development of genomic resources. Here we introduce the pea aphid and discuss a number of biological questions for which the species is well suited. We then review previous mapping and quantitative …

Management Recommendations Based On Matrix Projection Models: The Importance Of Considering Biological Limits, Joan Lubben, Brigitte Tenhumberg, Andrew J. Tyre, Richard Rebarber

School of Biological Sciences: Faculty Publications

Matrix population models are a common tool for evaluating different management strategies. In general, under deterministic analyses, management strategies are recommended that improve those matrix transitions that are most sensitive or elastic with respect to the asymptotic population growth rate, λ. These recommendations usually ignore the biological limit for these transitions. In this paper we use the endangered Serengeti cheetah (Acinonyx jubatus) as a case study to illustrate that ignoring biological limits leads to a recommendation that will not always achieve the desired goal of an asymptotic population growth rate, λ ≥ 1. We estimate the survivorships of …

Comparative Pollination Biology Of Sympatric And Allopatric Andean Iochroma (Solanaceae), Stacey Dewitt Smith, Steven J. Hall, Pablo R. Izquierdo, David A. Baum

School of Biological Sciences: Faculty Publications

Field studies were conducted for 15 species of Iochroma Benth, and the nested genus Acnistus Schott to quantify the diversity of pollination systems and to assess the potential contribution of pollinator behavior to the persistence of closely related species in sympatry. We combined measures of pollinator visitation and pollen deposition to estimate the importance of major groups of pollinators for each species, and we calculated proportional similarity in the pollinator assemblage among species. We found that 12 species of Iochroma, encompassing a range of flower colors and sizes, were principally pollinated by hummingbirds and, in many cases, by the …

Vulnerability Of Rehabilitated Agricultural Production Systems To Invasion By Nontarget Plant Species, Sara G. Baer, David M. Engle, Johannes M.H. Knops, Kenneth A. Langeland, Bruce D. Maxwell, Fabian D. Menalled, Amy J. Symstad

School of Biological Sciences: Faculty Publications

Vast areas of arable land have been retired from crop production and ‘‘rehabilitated’’ to improved system states through landowner incentive programs in the United States (e.g., Conservation and Wetland Reserve Programs), as well as Europe (i.e., Agri-Environment Schemes). Our review of studies conducted on invasion of rehabilitated agricultural production systems by nontarget species elucidates several factors that may increase the vulnerability of these systems to invasion. These systems often exist in highly fragmented and agriculturally dominated landscapes, where propagule sources of target species for colonization may be limited, and are established under conditions where legacies of past disturbance persist and …

Arabidopsis Drb4, Ago1, Ago7, And Rdr6 Participate In A Dcl4-Initiated Antiviral Rna Silencing Pathway Negatively Regulated By Dcl1, Feng Qu, Xiaohong Ye, Thomas Jack Morris

School of Biological Sciences: Faculty Publications

Plant RNA silencing machinery enlists four primary classes of proteins to achieve sequence-specific regulation of gene expression and mount an antiviral defense. These include Dicer-like ribonucleases (DCLs), Argonaute proteins (AGOs), dsRNA-binding proteins (DRBs), and RNA-dependent RNA polymerases (RDRs). Although at least four distinct endogenous RNA silencing pathways have been thoroughly characterized, a detailed understanding of the antiviral RNA silencing pathway is just emerging. In this report, we have examined the role of four DCLs, two AGOs, one DRB, and one RDR in controlling viral RNA accumulation in infected Arabidopsis plants by using a mutant virus lacking its silencing suppressor. Our …

A Novel Ecological Role Of The Firmicutes Identified In Thermophilic Microbial Fuel Cells, Kelly C. Wrighton, Peter Agbo, Falk Warnecke, Karrie A. Weber, Eoin L. Brodie, Todd Z. Desantis, Philip Hugenholtz, Gary L. Andersen, John D. Coates

School of Biological Sciences: Faculty Publications

Significant effort is currently focused on microbial fuel cells (MFCs) as a source of renewable energy. Most studies concentrate on operation at mesophilic temperatures. However, anaerobic digestion studies have reported on the superiority of thermophilic operation and demonstrated a net energy gain in terms of methane yield. As such, our studies focused on MFC operation and microbiology at 55 °C. Over a 100-day operation, these MFCs were stable and achieved a power density of 37mW m^–2 with a coulombic efficiency of 89%. To infer activity and taxonomic identity of dominant members of the electricity-producing community, we performed phylogenetic microarray …

Polygyny And Female Breeding Failure Reduce Effective Population Size In The Lekking Gunnison Sage-Grouse, Julie R. Stiver, Anthony D. Apa, Thomas E. Remington, Robert M. Gibson

School of Biological Sciences: Faculty Publications

Populations with small effective sizes are at risk for inbreeding depression and loss of adaptive potential. Variance in reproductive success is one of several factors reducing effective population size (N_e) below the actual population size (N). Here, we investigate the effects of polygynous (skewed) mating and variation in female breeding success on the effective size of a small population of the Gunnison sage-grouse (Centrocercus minimus), a ground nesting bird with a lek mating system. During a two-year field study, we recorded attendance of marked birds at leks, male mating success, the reproductive success …

Interspecific Demographic Trade-Offs And Soil-Related Habitat Associations Of Tree Species Along Resource Gradients, Sabrina E. Russo, Patrick Brown, Sylvester Tan, Stuart J. Davies

School of Biological Sciences: Faculty Publications

Summary

1. Interspecific relationships between fundamental demographic rates, often called demographic trade-offs, emerge from constraints within individuals related to morphology, physiology and resource allocation. Plant species that grow fast in high light usually have high mortality in shade, and this well-established relationship in part defines a species’ successional niche. More generally, this relationship represents a trade-off between a species’ ability to grow quickly to exploit abundant resources vs. avoiding mortality when resources are less plentiful, but few studies have described this demographic trade-off with respect to environmental factors other than light.

2. Using demographic data from 960 tree species in …

Corrigendum (Russo Et Al. 2007): A Re-Analysis Of Growth–Size Scaling Relationships Of Woody Plant Species, Sabrina E. Russo, Susan K. Wiser, David A. Coomes

School of Biological Sciences: Faculty Publications

Russo et al. (2007) tested two predictions of the Metabolic Ecology Model (Enquist et al. 1999, 2000) using a data set of 56 tree species in New Zealand: (i) the rate of growth in tree diameter (dD/dt) should be related to tree diameter (D) as dD/dt = βDα and (ii) tree height (H) should scale with tree diameter as H(D) = γDδ, where t is time, β and γ are scaling coefficients that may vary between species, and α and δ are invariant scaling exponents predicted to equal 1/3 and 2/3, respectively (Enquist et al. 1999, 2000). To this end, …

The Genome Sequence Of The Metal-Mobilizing, Extremely Thermoacidophilic Archaeon Metallosphaera Sedula Provides Insights Into Bioleaching-Associated Metabolism, Kathryne S. Auernik, Yukari Maezato, Paul H. Blum, Robert M. Kelly

School of Biological Sciences: Faculty Publications

Despite their taxonomic description, not all members of the order Sulfolobales are capable of oxidizing

reduced sulfur species, which, in addition to iron oxidation, is a desirable trait of biomining microorganisms.

However, the complete genome sequence of the extremely thermoacidophilic archaeon Metallosphaera sedula

DSM 5348 (2.2 Mb, _2,300 open reading frames [ORFs]) provides insights into biologically catalyzed metal

sulfide oxidation. Comparative genomics was used to identify pathways and proteins involved (directly or

indirectly) with bioleaching. As expected, the M. sedula genome contains genes related to autotrophic carbon

fixation, metal tolerance, and adhesion. Also, terminal oxidase cluster organization indicates the presence …

Geographic Distribution: Sphaerodactylus Elegans Elegans (Ashy Gecko). Usa: Florida: Broward Co., Louis A. Somma, Kenneth L. Krysko

Papers in Herpetology

FLORIDA: BROWARD County: Pembroke Pines: 1031 NW 93rd Ave (26.0168833°N, 80.2695694°W; WGS84; elev. <1 >m). October 27, 2007. Collected by Lisa A. Charlton. Verified by F. Wayne King, Florida Museum of Natural History, University of Florida. One neonate captured in Jackson sticky trap set to sample insects in an alee tree (Blighia sapida). UF 152418. New county record. Originally turned in to Division of Plant Industry (DPI), Florida Department of Agriculture and Consumer Services, Gainesville, Florida, on October 31, 2007; Entomology Log No. 8204. This nonindigenous gecko was flrst reported from Key West, Monroe County, Florida, more than 85 …

Ecological Genomics: Understanding Gene And Genome Function In The Natural Environment, M. C. Ungerer, L. C. Johnson, M. A. Herman

School of Biological Sciences: Faculty Publications

The field of ecological genomics seeks to understand the genetic mechanisms underlying responses of organisms to their natural environments. This is being achieved through the application of functional genomic approaches to identify and characterize genes with ecological and evolutionary relevance. By its very nature, ecological genomics is an interdisciplinary field. In this review, we consider the significance of this new area of study from both an ecological and genomic perspective using examples from the recent literature. We submit that by considering more fully an ecological context, researchers may gain additional insights into the underlying genetic basis of ecologically relevant phenotypic …

The Spectrum Of Mitochondrial Mutation Differs Across Species, Kristi L. Montooth, David M. Rand

School of Biological Sciences: Faculty Publications

Mutations are ubiquitous, and many arise during the very process of replicating and transmitting genomes. This process is the source of the genetic variation that provides the raw material for both evolutionary novelty and human disease. Mutation rates are known to vary among nucleotides, across genomic regions, and between taxa. It is conventional wisdom that animal mitochondrial DNA (mtDNA) is one genomic region that has a particularly high mutation rate. Until recently, this high rate of mutation has been predominantly inferred from high levels of mitochondrial sequence divergence between species. However, the apparently simple process of mutation and sequence divergence …

Rapid Rates Of Lineage-Specific Gene Duplication And Deletion In The Α-Globin Gene Family, Federico G. Hoffmann, Juan C. Opazo, Jay F. Storz

Jay F. Storz Publications

Phylogeny reconstructions of the globin gene families have revealed that paralogous genes within species are often more similar to one another than they are to their orthologous counterparts in closely related species. This pattern has been previously attributed to mechanisms of concerted evolution such as interparalog gene conversion that homogenize sequence variation between tandemly duplicated genes and therefore create the appearance of recent common ancestry. Here we report a comparative genomic analysis of the α-globin gene family in mammals that reveal a surprisingly high rate of lineage-specific gene duplication and deletion via unequal crossing-over. Results of our analysis reveal that …

Molecular Evolution Of Cytochrome B In High- And Low-Altitude Deer Mice (Genus Peromyscus), E.J. Gering, J. C. Opazo, Jay F. Storz

Jay F. Storz Publications

Patterns of amino-acid polymorphism in human mitochondrial genes have been interpreted as evidence for divergent selection among populations that inhabit climatically distinct environments. If similar patterns are mirrored in other broadly distributed mammalian species, then adaptive modifications of mitochondrial protein function may be detected in comparisons among locally adapted populations of a single wide-ranging species, or among closely related species that have adapted to different environments. Here, we test for evidence of positive selection on cytochrome b variation within and among species of the ecologically diverse rodent genus Peromyscus. We used likelihood-based comparisons of synonymous and nonsynonymous substitution rates …

Improving The Reliability Of Molecular Sexing Of Birds Using A W-Specific Marker, Daizaburo Shizuka, Bruce E. Lyon

Papers in Ornithology

Molecular techniques for identifying sex of birds utilize length differences between CHD-Z and CHD-W introns, but in some cases these methods can lead to sexing errors. Here we show that an additional W-specific primer can be used in conjunction with a pre-existing sexing primer pair to dramatically improve the reliability of molecular sexing methods. We illustrate the approach with American coots (Fulica americana), a species with CHD-Z polymorphism that could not be accurately sexed using traditional methods. We developed a reverse primer GWR2 designed to sit within the intron of the W chromosome and amplify a distinctively small …

The Fha Domain Proteins Dawdle In Arabidopsis And Snip1 In Humans Act In Small Rna Biogenesis, Bin Yu, Binglian Zheng, Lijuan Ji, David Chevalier, Manu Agarwal, Vanitharani Ramachandran, Wanxiang Li, Thierry Lagrange, John C. Walker, Xuemei Chen

Bin Yu Publications

Proteins containing the forkhead-associated domain (FHA) are known to act in biological processes such as DNA damage repair, protein degradation, and signal transduction. Here we report that DAWDLE (DDL), an FHA domain-containing protein in Arabidopsis, acts in the biogenesis of miRNAs and endogenous siRNAs. Unlike mutants of genes known to participate in the processing of miRNA precursors, such as dcl1, hyponastic leaves1, and serrate, ddl mutants show reduced levels of pri-miRNAs as well as mature miRNAs. Promoter activity of MIR genes, however, is not affected by ddl mutations. DDL is an RNA binding protein and is able …

Presidential Address: Nothing Succeeds Like Excess, Steven A. Nadler

Harold W. Manter Laboratory of Parasitology: Faculty Publications

To the members of the American Society of Parasitologists, I offer my appreciation for the opportunity to serve as your president. When I was notified of my successful election as an officer, it brought to mind that famous remark by Adlai Stevenson who said, ‘‘In America, anybody can be president. That’s one of the risks you take.’’ So, what I initially perceived as somewhat of a risky venture, proved to be a more valuable and interesting experience than I anticipated. Let’s hope that my presidential address has a similar outcome.

Muscleworms, Parelaphostrongylus Andersoni (Nematoda: Protostrongylidae), Discovered In Columbia White-Tailed Deer From Oregon And Washington: Implications For Biogeography And Host Associations, Ingrid M. Asmundsson, Jack A. Mortenson, Eric P. Hoberg

Harold W. Manter Laboratory of Parasitology: Faculty Publications

Parelaphostrongylus andersoni is considered a characteristic nematode infecting white-tailed deer (Odocoileus virginianus). Host and geographic distribution for this parasite, however, remain poorly defined in the region of western North America. Fecal samples collected from Columbia white-tailed deer (O. v. leucurus) in a restricted range endemic to Oregon and Washington, USA, were examined for dorsal-spined larvae characteristic of many protostrongylid nematodes. Multilocus DNA sequence data (internal transcribed spacer 2 and cytochrome c oxidase subunit 1) established the identity and a new record for P. andersoni in a subspecies of white-tailed deer previously unrecognized as hosts. Populations of …